scholarly journals Investigations on spectroscopic characterizations, molecular docking, NBO, drug-Likeness, and ADME properties of 4H-1,2,4-triazol-4-amine by combined computational approach

2021 ◽  
Vol 12 (4) ◽  
pp. 401-411
Author(s):  
Sibel Celik ◽  
Senay Yurdakul
Keyword(s):  
Molecular Docking ◽  
Density Functional ◽  
Growth Factor Receptor ◽  
Dft Method ◽  
Frontier Molecular Orbital ◽  
Spectral Studies ◽  
Visible Absorption ◽  
Charge Delocalization ◽  
Adme Properties ◽  
Orbital Analysis

In this study, the spectroscopic characterization, frontier molecular orbital analysis, and natural bond orbital analysis (NBO) analysis were executed to determine the movement of electrons within the molecule and the stability, and charge delocalization of the 4H-1,2,4-triazol-4-amine (4-AHT) through density functional theory (DFT) approach and B3LYP/6-311++G(d,p) level of theory. Surface plots of the hybrids’ Molecular Electrostatic Potential (MEP) revealed probable electrophilic and nucleophilic attacking sites. The discussed ligand were observed to be characterized by various spectral studies (FT-IR, UV-Vis). The calculated IR was found to be correlated with experimental values. The UV-Vis data of the molecule was used to analyze the visible absorption maximum (λmax) using the time-dependent DFT method. Since the principle of drug-likeness is usually used in combinatorial chemistry to minimize depletion in pharmacological investigations and growth, drug-likeness and ADME properties were calculated in this research to establish 4-AHT molecule bioavailability. Furthermore, molecular docking studies were carried out. Molecular docking analysis was performed for the title ligand inside the active site of the Epidermal Growth Factor Receptor (EGFR). The title compound’s anti-tumor activity against the cancer cell, in which EGFR is strongly expressed, prompted us to conduct molecular docking into the ATP binding site of EGFR to predict whether this molecule has an analogous binding mode to the EGFR inhibitors (PDB: ID: 1M17).

Theoretical investigation on tautomerism and NLO properties of Salicylideneaniline derivatives

2021 ◽  
Author(s):  
N. Daho ◽  
N. Benhalima ◽  
F. KHELFAOUI ◽  
O. SADOUKI ◽  
M. Elkeurti ◽  
...  
Keyword(s):  
Optical Properties ◽  
Density Functional ◽  
Energy Gap ◽  
Intramolecular Proton Transfer ◽  
Basis Set ◽  
Frontier Molecular Orbital ◽  
Molecular Orbital Calculations ◽  
Visible Absorption ◽  
Charge Delocalization ◽  
Intramolecular Hydrogen

In this work, a comprehensive investigation of the salicylideneaniline derivatives is carried out using density functional theory to determine their linear and non-linear optical properties. Geometry optimizations, for gas and solvent phases, of the tautomers (enol and keto forms) are calculated using B3LYP levels with 6–31G (d,p) basis set . An intramolecular proton transfer, for 1SA-E and 2SA-E, is performed by a PES scan process at the B3LYP/6-31G (d,p) level. The optical properties are determined and show that they have extremely high nonlinear optical properties. In addition, the RDG analysis, MEP, and gap energy are calculated. The low energy gap value indicates the possibility of intramolecular charge transfer. The frontier molecular orbital calculations clearly show the inverse relationship of HOMO–LUMO gap with the first-order hyperpolarizability (β = 59.6471 × 10-30 esu), confirming that the salicylideneaniline derivatives can be used as attractive future NLO materials. Therefore, the reactive sites are predicted using MEP and the visible absorption maxima are analyzed using a theoretical UV–Vis spectrum. Natural bond orbitals are used to investigate the stability, charge delocalization, and intramolecular hydrogen bond.

scholarly journals Molecular Structures and Spectral Properties of Natural Indigo and Indirubin: Experimental and DFT Studies

Molecules ◽  
2019 ◽  
Vol 24 (21) ◽  
pp. 3831 ◽  
Author(s):  
Zixin Ju ◽  
Jie Sun ◽  
Yanping Liu
Keyword(s):  
Density Functional Theory ◽  
Spectral Properties ◽  
Density Functional ◽  
Dft Method ◽  
Molecular Structures ◽  
Basis Set ◽  
Frontier Molecular Orbital ◽  
Visible Absorption ◽  
Functional Theory ◽  
Uv Visible

This paper presents a comparative study on natural indigo and indirubin in terms of molecular structures and spectral properties by using both computational and experimental methods. The spectral properties were analyzed with Fourier transform infrared (FTIR), Raman, UV-Visible, and fluorescence techniques. The density functional theory (DFT) method with B3LYP using 6-311G(d,p) basis set was utilized to obtain their optimized geometric structures and calculate the molecular electrostatic potential, frontier molecular orbitals, FTIR, and Raman spectra. The single-excitation configuration interaction (CIS), time-dependent density functional theory (TD-DFT), and polarization continuum model (PCM) were used to optimize the excited state structure and calculate the UV-Visible absorption and fluorescence spectra of the two molecules at B3LYP/6-311G(d,p) level. The results showed that all computational spectra agreed well with the experimental results. It was found that the same vibrational mode presents a lower frequency in indigo than that in indirubin. The frontier molecular orbital analysis demonstrated that the UV-Visible absorption and fluorescence bands of indigo and indirubin are mainly derived from π → π* transition. The results also implied that the indigo molecule is more conjugated and planar than indirubin, thereby exhibiting a longer maximum absorption wavelength and stronger fluorescence peak.

scholarly journals Density functional theory calculations and Hirshfeld surface analysis of propyl-para-hydroxybenzoate (PHB) for optoelectronic application

2020 ◽  
Vol 0 (0) ◽  
Author(s):  
V. Mohankumar ◽  
N. Karunagaran ◽  
M. Senthil Pandian ◽  
P. Ramasamy
Keyword(s):  
Charge Transfer ◽  
Surface Analysis ◽  
Density Functional ◽  
Hirshfeld Surface ◽  
Basis Set ◽  
Hirshfeld Surface Analysis ◽  
Frontier Molecular Orbital ◽  
Mulliken Charge ◽  
Charge Analysis ◽  
Orbital Analysis

AbstractThe geometries, electrostatic potential, Mulliken charge analysis, Natural Bond Orbital analysis and polarizabilities of propyl-para-hydroxybenzoate were calculated using B3LYP functional with 6-311++G(d,p) basis set. The calculated geometries are well matched with the experimental values. The Mullliken atomic charge analysis shows that the eventual charges are contained in the molecule. The NBO analysis explains the intramolecular charge transfer in the PHB molecule. The bonding features of the molecule were analyzed with the aid of Hirshfeld surface analysis. The frontier molecular orbital analysis showed the charge transfer obtained within the molecule. The calculated hyperpolarizability of the PHB molecule was 6.977E−30 esu and it was 8.9 times that of standard urea molecule.

scholarly journals Physiochemical, molecular docking, and pharmacokinetic studies of Naproxen and its modified derivatives based on DFT

2018 ◽  
Vol 6 (09) ◽  
Author(s):  
Monir Uzzaman ◽  
Mohammed Jabedul Hoque
Keyword(s):  
Molecular Docking ◽  
Binding Affinity ◽  
Density Functional ◽  
Parent Drug ◽  
Electronic Energy ◽  
Frontier Molecular Orbital ◽  
Pharmacokinetic Studies ◽  
Biochemical Interaction ◽  
Gibb’S Free Energy ◽  
Anti Inflammation

Naproxen (N) is a member of nonsteroidal anti-inflammation drug and widely used as an analgesic, antipyretic, and anti-inflammation agent. In this investigation, the inherent stability and biochemical interaction of Naproxen and its related molecules have been studied. Density functional theory (DFT) with B3LYP/ 6-31G (d, p) has been employed to optimize the structures. Frontier molecular orbital features (HOMO-LUMO gap, hardness, softness), dipole moment, electrostatic potential and thermodynamic properties (electronic energy, enthalpy, Gibb’s free energy) of these optimized drugs are investigated. Molecular docking has been performed against prostaglandin H2 (PGH2) synthase protein 5F19 to search the binding affinity and mode(s) of all compounds. It is found that, all compounds are thermodynamically stable; some of them are chemically more reactive and show better binding affinity than the parent drug. ADMET calculations predict the improved pharmacokinetic properties of all compounds. Finally, this study can be helpful for the design of new analgesic, antipyretic drug.

scholarly journals Molecular Modeling of Interactions between N-(Carboxymethyl)-N-tetradecylglycine and Fluorapatite

Minerals ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 278 ◽  
Author(s):  
Nan Nan ◽  
Yimin Zhu ◽  
Yuexin Han ◽  
Jie Liu
Keyword(s):  
Density Functional ◽  
Density Functional Theory Calculation ◽  
Service Condition ◽  
Frontier Molecular Orbital ◽  
Adsorption Ability ◽  
Functional Theory ◽  
Molecular Orbital Analysis ◽  
Theory Calculation ◽  
Orbital Analysis ◽  
Flotation Collector

In this study, a flotation collector N-(carboxymethyl)-N-tetradecylglycine (NCNT) was introduced for the purpose of energy-saving, and its adsorption ability on a fluorapatite (001) surface was investigated by density functional theory calculation. The results of frontier molecular orbital analysis of NCNT and adsorption energy between NCNT and fluorapatite (FAp) showed that NCNT possessed better activity and stronger interactions in the reagent–FAp system than oleic acid (OA). A simulation model revealed that the adsorption positions of NCNT on the fluorapatite surface are calcium atoms, at which NCNT chemisorbed on (001) fluorapatite surface via a bidentate geometry involving the formation of two Ca–O bonds. Flotation experiments verified that NCNT had a good recovery of 92.27% on FAp at pH 3.5, which was slightly lower than OA. Moreover, NCNT was used at 16 °C, which was much lower than the OA’s service condition (25 °C).

scholarly journals Zinc-Doped Boron Phosphide Nanocluster as Efficient Sensor for SO2

2020 ◽  
Vol 2020 ◽  
pp. 1-12 ◽  
Author(s):  
Shahid Hussain ◽  
Shahzad Ali Shahid Chatha ◽  
Abdullah Ijaz Hussain ◽  
Riaz Hussain ◽  
Muhammad Yasir Mehboob ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Frontier Molecular Orbital ◽  
Functional Theory ◽  
Global Indices ◽  
Boron Phosphide ◽  
Adsorption Energies ◽  
Molecular Orbital Analysis ◽  
Orbital Analysis ◽  
Optimized Geometries

Adsorption of SO2 on pure B12P12 and Zn-doped B12P12 is investigated through density functional theory methods. Zn adsorption on BP delivers four optimized geometries: B-Top, P-top, b64, and ring-enlarged geometry with adsorption energies of −57.12 kJ/mol, −14.50 kJ/mol, −22.94 kJ/mol, and −14.83 kJ/mol, respectively. The adsorption energy of SO2 on pristine boron phosphide is −14.92 kJ/mol. Interaction of SO2 with Zn-doped boron phosphide gives four different geometries with adsorption energies of −69.76 kJ/mol, −9.82 kJ/mol, −104.92 kJ/mol, and −41.87 kJ/mol. Geometric parameters such as dipole moment, QNBO, frontier molecular orbital analysis, PDOS, and global indices of reactivity are performed to visualize the changes in electronic properties of B12P12 after Zn and SO2 adsorption.

scholarly journals Spectroscopic Examination using Density Functional Theory Calculations on 3-chloro-5-methoxyphenol

2020 ◽  
Vol 8 (4S4) ◽  
pp. 113-118
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Density Functional Theory Method ◽  
Density Functional Theory Calculations ◽  
Nbo Analysis ◽  
Computational Method ◽  
Frontier Molecular Orbital ◽  
Functional Theory ◽  
Charge Delocalization ◽  
Raman Spectral Data

The complete vibrational assignment of 3-chloro-5-methoxyphenol (CMOP) has been identified by the observed IR and Raman spectral data and vibrational frequencies were calculated by density functional theory method. The ability of the computational method for describing the vibrational modes can be understood by comparing experimental and theoretical spectra. Besides, frontier molecular orbital, Mulliken’s charge analyses and molecular electrostatic potential (MEP) surfaces have been computed. The natural bond orbital (NBO) analysis has been studied to analyze the charge delocalization and molecular hyperconjugative interactions

X-ray and DFT Investigation of (E)-4-bromo-5-methoxy-2-((o-tolylimino)methyl)phenol Compound

2018 ◽  
pp. 454-461
Keyword(s):  
Density Functional ◽  
Theoretical Calculations ◽  
Population Analysis ◽  
Diffraction Method ◽  
Dft Method ◽  
Basis Set ◽  
X Ray Diffraction ◽  
Mulliken Population ◽  
Charge Delocalization ◽  
X Ray

(E)-4-bromo-5-methoxy-2-((o-tolylimino)methyl)phenol was investigated by experimental and theoretical methodologies. The solid state molecular structure was determined by X-ray diffraction method. All theoretical calculations were performed by density functional theory (DFT) method by using B3LYP/6-31G(d,p) basis set. The titled compound showed the preference of enol form, as supported by X-ray diffraction method. The geometric and molecular properties were compaired for both enol-imine and keto-amine forms for title compound. Stability of the molecule arises from hyperconjugative interactions, charge delocalization and intramolecular hydrogen bond has been analyzed using natural bond orbital (NBO) analysis. Mulliken population method and natural population analysis (NPA) have been studied. Also, condensed Fukui function and relative nucleophilicity indices calculated from charges obtained with orbital charge calculation methods (NPA). Molecular electrostatic potential (MEP) and non linear optical (NLO) properties are also examined.

Computational, Experimental Structural Characterization and Molecular Docking Studies of 5,7-Dihydroxy-4-methoxyflavone against Cytochrome P450 Enzymes

2020 ◽  
Vol 5 (3) ◽  
pp. 197-207
Author(s):  
A. Harikrishnan ◽  
R. Madivanane
Keyword(s):  
Cytochrome P450 ◽  
Molecular Docking ◽  
Title Compound ◽  
Density Functional ◽  
Geometry Optimization ◽  
Dft Method ◽  
Cytochrome P450 Enzymes ◽  
Molecular Docking Study ◽  
Experimental Values ◽  
Vibrational Wavenumbers

In this work, the geometry optimization and harmonic vibrational wavenumbers of kaempferide (5,7-dihydroxy-4-methoxyflavone) were computed by density functional theory (DFT) method. Theoretically computed vibrational wavenumbers were compared with experimental values and the interpretation of the vibrational spectra has been studied. Frontier molecular orbitals (FMO) and molecular electrostatic potential (MEP) analysis of the title compound have been carried out. The 1H & 13C NMR, UV visible and electronic properties of the compound were investigated theoretically and compared with the experimental values. Molecular docking study of the compound against cytochrome P450 family enzymes (CYPs 1A1, 1A2, 3A4, 2C8, 2C9 and 2D6) were also studied and the results revealed that the title compound interact with human CYP2C8 enzymes with minimum binding energy of -9.43 kcal/mol. The compound forms hydrogen bond with the residues of Thr302, Thr305, Leu361, Val362, Cys435, Gln356 and Ala297. Thus, these studies assist to understand the inhibitory mechanism of kaempferide with CYP450 enzymes and may facilitate significant clinical implications in the prevention and treatment of various therapeutic diseases.

Vibrational and electronic profiles, molecular docking and biological prediction of 5-methoxy-1-[(5-methoxy- 1H-indol-2-yl)methyl]-1H-indole: Experimental and theoretical investigations

2016 ◽  
Vol 15 (06) ◽  
pp. 1650046
Author(s):  
Nadia G. Haress ◽  
Devarasu Manimaran ◽  
Isaac Hubert Joe ◽  
Aida A. EL-Azzouny ◽  
Reem I. Al-Wabli ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Density Functional ◽  
Orbital Energy ◽  
Potential Energy Distribution ◽  
Immunomodulatory Activity ◽  
Equilibrium Geometry ◽  
Distribution Analysis ◽  
Charge Delocalization ◽  
Docking Approach ◽  
Privileged Structures

Indole derivatives represent an important class of privileged structures. Spectroscopic (Fourier transform infrared (FT-IR), FT-Raman, 1H and [Formula: see text]C nuclear magnetic resonance (NMR)) investigations of the indole-bearing title compound, namely 5-methoxy-1-[(5-methoxy-1[Formula: see text]-indol-2-yl)methyl]-1[Formula: see text]-indole (MMIMI) have been carried out. The corresponding data of the MMIMI molecule were analyzed to understand its optimized geometry, and inter/intra-molecular interactions. The equilibrium geometry, harmonic vibrational wavenumbers, Frontier orbital energy, and natural bond orbital (NBO) analyses have been performed with the help of density functional theory (DFT) with B3LYP/6-311[Formula: see text]G([Formula: see text],[Formula: see text]) level of theory. The vibrational modes have been unequivocally assigned using potential energy distribution analysis. The theoretically predicted wavenumbers have good agreement with the experimental values. NBO has confirmed the intra-molecular charge transfer interactions. HOMO–LUMO analysis was carried out to explore charge delocalization on the MMIMI molecule. The immunomodulatory activity of the title molecule was predicted using molecular docking approach.

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